If you use the extra SATA ports on the motherboard (located near the fan) and have a dual/triple/etc boot with another OS, the additional OS’s will not recognize the drives. The Apple EFI BIOS will automatically set the other OS’s to go into Legacy mode instead of AHCI. You can use a grub bootloader to tweak the settings for Windows/Linux and trick it into going to AHCI mode, but then you will have to reinstall the OS with a driver disk (along with Intel AHCI drivers…See “RAID” drivers on Intel’s website).

If you use the extra ports for an Optical drive (Blueray), then be aware utilities like Toast will not work with Blueray. Roxio Toast does not recognize SATA buses in viewing Blueray and there are reported problems with burning (Of course Windows won’t see the drive at all). If you want Blueray for burning/viewing get a drive that’s EIDE/IDE/PATA or buy an IDE/SATA converter. If you use the SATA ports for extra drives only seen by Apple (ESATA), then everything should work fine. I’m testing a LG GGW-H20L Blueray/HD-DVD/DVD/Lightscribe (SATA drive) player now. I’ve ordered a SATA/IDE from http://www.cooldrives.com/sahadradtoid.html since it seems to fit inside of the MacPro’s confined space. I’ll let you know how it turns out.

P.S.

I’m not 100% sure that Fusion or Parallels will see the ESATA drives.

*** Update ***
I received the IDE/SATA converter. It’s an easy install *IF* you’re planning on only 1 drive in the bay. If you have two drives, get a power splitter or an short 3 inch power extender cable. Then try to work that blasted thing in. You’ll know what I mean when you try it. Geez.
Anyway, everything seems to work in Windows and the Mac side now. I even ran a firmware update on the drive from inside Windows Vista64.